Such systems aim to analyze models, to design models, or to simulate and understand the emergent properties of complex normal and pathological living systems in order to propose a global dynamic and predictive vision.
A merging process consists in choosing which entities from input models must be grouped in the output model.
FIGS. 1, 2 and 3 illustrate a composition of models A (FIG. 1) and B (FIG. 2) for delivering an output model AB (FIG. 3). On this example, common entities are named Mp and P0. On these figures, squares represent interactions between entities. The output model AB depends on which entities are supposed to be identified in both A and B models.
This series of choices is a non-trivial process, for various reasons (a same biological phenomenon may have different modeling, models may have been made by different people, with different naming conventions, . . . ). Many criterions can be used to help making these choices, as molecules names, annotations or graph topology.
Annotations are additional data attached to the model elements which add unstructured information to the model, mostly using a text format. For instance, annotations can be used to add references to public databases. Such databases are very commonly used in the bioinformatics field.
The database provided under the trademark Uniprot is an example of a large and widely-used protein database. Each database has its own unique identifier syntax. For instance, a protein of a model could have an annotation “uniprot:P38731”. The identifier “P38731” is Uniprot-specific and refers to an object in the Uniprot database: http://www.uniprot.org/uniprot/P38731 (“Siderophore iron transporter ARN1”). As these annotations are added by a user without any consistency-check, they may contain numerous errors. Moreover, some clones or ambiguities exist in public databases. These two points explain why even with fully-annotated models, merging is not a straightforward process.
The merging process can either be manual or automated by algorithms, in which case the result may contain errors and, as a result, needs a manual curing.